Not really. तुमको क्या चाहिए (can also be written तुम्हें क्या चाहिए) may be directed towards a person of either gender. It could mean 'What do you want' but the meaning is closer to 'What do you need?'. Basically, it conveys a stronger sentiment.
As you say, तुम क्या चाहती हो? is directed towards a female person due to the feminine form of the verb. The masculine form would be 'तुम क्या चाहते हो?'. Both of these mean 'What do you want?'.
तुम and आप conjugate similar to plurals even though they might be referring to just one person. So, you need to use the masculine plural form चाहते and not the singular form चाहता.
तू conjugates similar to singular nouns so it will be तू क्या चाहता है (m) or तू क्या चाहती है (f).